LAMMPS (10 Mar 2021)
  using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules

units		lj
atom_style      bond
boundary        p p f

lattice		fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region          box block 0 5 0 5 0 10
create_box      3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
  1 by 1 by 4 MPI processor grid

region		substrate block INF INF INF INF INF 3
create_atoms	1 region substrate
Created 350 atoms
  create_atoms CPU = 0.139 seconds

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0
pair_coeff	1 2 1.0 1.0 5.0
mass		* 1.0

bond_style	harmonic
bond_coeff      1 5.0 1.0

neigh_modify	delay 0

molecule        dimer molecule.dimer
Read molecule template dimer:
  1 molecules
  2 atoms with max type 3
  1 bonds with max type 1
  0 angles with max type 0
  0 dihedrals with max type 0
  0 impropers with max type 0
region          slab block 0 5 0 5 8 9

group		addatoms empty
0 atoms in group addatoms
region          mobile block 0 5 0 5 2 INF
group		mobile region mobile
150 atoms in group mobile

compute	add addatoms temp
compute_modify	add dynamic/dof yes extra/dof 0

fix		1 addatoms rigid/small molecule mol dimer
  create bodies CPU = 0.006 seconds
  0 rigid bodies with 0 atoms
  1.0000000 = max distance from body owner to body atom
fix		2 mobile langevin 0.1 0.1 0.1 587283
fix		3 mobile nve

fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0 rigid 1
fix		5 addatoms wall/reflect zhi EDGE

thermo_style	custom step atoms temp epair etotal press
thermo          100
thermo_modify	temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)

#dump		1 all atom 50 dump.deposit.atom

#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	2 pad 5

#dump		3 all movie 50 tmp.mpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	3 pad 5

run             10000
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.3
  ghost atom cutoff = 5.3
  binsize = 2.65, bins = 3 3 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
Step Atoms Temp E_pair TotEng Press 
       0      350            0   -6.9215833   -6.9215833   -1.0052629 
     100      352    1.0079368   -6.8946578   -6.8874992  -0.73775337 
     200      354    1.0081552   -6.8645575    -6.850318  -0.69629729 
     300      356    1.0085803    -6.821677   -6.8004288  -0.69532657 
     400      358    1.0099188   -6.7837923   -6.7555822  -0.68879568 
     500      360    1.0140221   -6.7446709   -6.7094618  -0.72991641 
     600      362     1.026146   -6.7129201   -6.6704003  -0.67063836 
     700      364    1.0683193   -6.6776523   -6.6262908  -0.65572472 
     800      366    1.0958893   -6.6402029   -6.5803182  -0.66307281 
     900      368    1.1231768   -6.6050912   -6.5364187  -0.64076928 
    1000      370    1.1976283   -6.5942507   -6.5133299  -0.69249019 
    1100      372    1.0506263   -6.5772313    -6.499564  -0.63072939 
    1200      374   0.93724351   -6.5732957   -6.4981157  -0.64963897 
    1300      376   0.93899686   -6.5578406   -6.4766773  -0.65096289 
    1400      378    0.8704974   -6.5468498   -6.4662482  -0.67613931 
    1500      380   0.84490693   -6.5401094   -6.4567304  -0.64385968 
    1600      382    0.9243154   -6.5611604   -6.4643734  -0.62096869 
    1700      384   0.67202953   -6.5590557   -6.4846775  -0.67807465 
    1800      386    0.8712464   -6.5654953   -6.4639251  -0.65860236 
    1900      388   0.70011668   -6.5808612    -6.495151  -0.65146463 
    2000      390   0.64019295   -6.5652168   -6.4831408  -0.70291888 
    2100      392   0.67578277   -6.5596196    -6.469113  -0.63315981 
    2200      394   0.60785287    -6.558941   -6.4740885   -0.7133822 
    2300      396    0.8155086   -6.5756022   -6.4571887  -0.69176417 
    2400      398   0.69028748   -6.5875474    -6.483484  -0.63743938 
    2500      400    0.5013913   -6.5871851   -6.5088427  -0.65872179 
    2600      402   0.51268385   -6.5782356    -6.495339  -0.74289067 
    2700      404   0.57745388   -6.5815718   -6.4850912  -0.67922914 
    2800      406   0.47317895   -6.5974978   -6.5159152  -0.64657562 
    2900      408   0.50593124   -6.6019054   -6.5120034  -0.64211427 
    3000      410   0.44423233   -6.5956684   -6.5144064  -0.66526127 
    3100      412   0.40808865   -6.5949863   -6.5182221  -0.62722445 
    3200      414   0.40692632   -6.5866689   -6.5080358  -0.76440608 
    3300      416   0.43908529   -6.5851721   -6.4980939  -0.69345883 
    3400      418   0.53825907   -6.5880076    -6.478553  -0.69726204 
    3500      420   0.46363057   -6.6135193   -6.5169296  -0.58015901 
    3600      422   0.39262699    -6.621857   -6.5381213  -0.74921264 
    3700      424   0.42679205   -6.6146579   -6.5215488  -0.69040431 
    3800      426   0.38997492   -6.6139725   -6.5270063  -0.78237667 
    3900      428    0.5222531   -6.6403886   -6.5214174  -0.78298122 
    4000      430   0.47841128   -6.6502681   -6.5390097  -0.68125967 
    4100      432   0.44609186   -6.6610827   -6.5552392  -0.81157037 
    4200      434    0.4591431   -6.6858064   -6.5747234  -0.79000753 
    4300      436   0.40690573   -6.6800195    -6.579693   -0.6781696 
    4400      438   0.43023944   -6.6849804   -6.5769294   -0.7620548 
    4500      440   0.40889421   -6.6783124   -6.5737656   -0.8577593 
    4600      442   0.41452051   -6.6968565   -6.5890061  -0.70427746 
    4700      444   0.36740394   -6.6920933   -6.5948636  -0.69303162 
    4800      446   0.40112316   -6.6869413   -6.5790158  -0.84792822 
    4900      448   0.42437165   -6.6789835   -6.5629444  -0.82278531 
    5000      450   0.41822898   -6.6770254   -6.5608507  -0.72224472 
    5100      452   0.38445688   -6.6738997   -6.5654522   -0.7022418 
    5200      454   0.39998238   -6.6670536   -6.5525212  -0.73639959 
    5300      456   0.39471029   -6.6728592   -6.5581681  -0.70419927 
    5400      458   0.35817807   -6.6702423   -6.5646658  -0.81657219 
    5500      460   0.37151428   -6.6690855    -6.558035  -0.78076653 
    5600      462   0.32642513   -6.6622352   -6.5633185  -0.69118644 
    5700      464   0.43665879   -6.6811227   -6.5470195  -0.77500043 
    5800      466   0.40704721   -6.6858874   -6.5592311  -0.72683597 
    5900      468    0.3861903   -6.6896953   -6.5679794  -0.78001958 
    6000      470   0.34073346   -6.6833717    -6.574627  -0.78170837 
    6100      472   0.39953874   -6.7083668   -6.5792785  -0.81791744 
    6200      474   0.36685189   -6.7114648   -6.5915027  -0.80545451 
    6300      476   0.35851799   -6.7261023    -6.607475  -0.77350495 
    6400      478   0.41771823   -6.7427425   -6.6029205  -0.85319003 
    6500      480   0.36519478    -6.732662   -6.6090284  -0.78712805 
    6600      482   0.30669571   -6.7269784   -6.6219892  -0.76698134 
    6700      484    0.3384344   -6.7261448   -6.6090213  -0.79935239 
    6800      486   0.36420902   -6.7320259   -6.6046277  -0.84650552 
    6900      488   0.40181215   -6.7490619   -6.6070279  -0.75753238 
    7000      490   0.30536068   -6.7398924   -6.6308351  -0.73210162 
    7100      492   0.28813004   -6.7257287   -6.6217794  -0.92178435 
    7200      494   0.30956277   -6.7342688   -6.6214727  -0.77532949 
    7300      496   0.36625115   -6.7528159   -6.6180561  -0.76247835 
    7400      498   0.30935271   -6.7401433   -6.6252231  -0.82809158 
    7500      500   0.33222282   -6.7410421   -6.6164585  -0.81948236 
    7600      502   0.33318693   -6.7488106    -6.622704  -0.82395904 
    7700      504   0.34570598   -6.7547394   -6.6226989  -0.85644369 
    7800      506   0.34587242   -6.7446006   -6.6113099  -0.82476511 
    7900      508    0.2969166   -6.7305429   -6.6151078   -0.8210214 
    8000      510   0.32355758   -6.7437629   -6.6168776  -0.81719054 
    8100      512   0.33784479   -6.7545537   -6.6209335  -0.78082067 
    8200      514   0.32351289   -6.7525032   -6.6234757  -0.87093587 
    8300      516   0.31900134   -6.7550972   -6.6268166  -0.79928704 
    8400      518    0.3338521   -6.7588757   -6.6235302  -0.81699503 
    8500      520   0.33115184   -6.7614854   -6.6261589  -0.79958489 
    8600      522   0.29478929   -6.7490188   -6.6276018  -0.81954456 
    8700      524     0.267993   -6.7467764   -6.6355389  -0.76642994 
    8800      526   0.28792085   -6.7527118   -6.6322887  -0.86911619 
    8900      528   0.32430992     -6.75901   -6.6223453  -0.87087898 
    9000      530   0.33151321   -6.7534845   -6.6127478  -0.79309499 
    9100      532   0.32760982   -6.7599992   -6.6199028   -0.7506309 
    9200      534   0.32579101   -6.7671489   -6.6268269  -0.94238755 
    9300      536   0.35144354   -6.7782581    -6.625813  -0.77952234 
    9400      538   0.33689976   -6.7804455   -6.6332867  -0.75768501 
    9500      540    0.3052486   -6.7745436   -6.6402908  -0.89621525 
    9600      542   0.30617581   -6.7648172   -6.6292412  -0.90623541 
    9700      544   0.30097715   -6.7714379   -6.6372707  -0.85534149 
    9800      546   0.31297479   -6.7814978   -6.6410604  -0.88651064 
    9900      548   0.31832347    -6.790661   -6.6468926       -1.006 
   10000      550   0.29239559   -6.7823137   -6.6494066   -1.0337518 
Loop time of 34.7661 on 4 procs for 10000 steps with 550 atoms

Performance: 124259.065 tau/day, 287.637 timesteps/s
73.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0076709  | 3.1286     | 9.1834     | 211.7 |  9.00
Bond    | 0.0040276  | 0.010416   | 0.022169   |   7.0 |  0.03
Neigh   | 0.052413   | 1.5948     | 4.885      | 155.3 |  4.59
Comm    | 4.9736     | 12.242     | 20.073     | 166.2 | 35.21
Output  | 0.053549   | 0.10104    | 0.21642    |  21.0 |  0.29
Modify  | 13.435     | 16.191     | 23.851     | 110.0 | 46.57
Other   |            | 1.499      |            |       |  4.31

Nlocal:        137.500 ave         299 max           2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost:        1898.75 ave        2679 max         524 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs:        9204.00 ave       23014 max           0 min
Histogram: 2 0 0 0 0 1 0 0 0 1

Total # of neighbors = 36816
Ave neighs/atom = 66.938182
Ave special neighs/atom = 0.36363636
Neighbor list builds = 832
Dangerous builds = 0
Total wall time: 0:00:34
